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Merged
jonasscheid merged 10 commits into from
Jan 9, 2026
Merged

Merge template 3.5.1 #429

jonasscheid merged 10 commits into from
Jan 9, 2026

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@jonasscheid jonasscheid commented Jan 8, 2026

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jan 8, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3ff11ef

+| ✅ 296 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-08 17:43:37

marissaDubbelaar
marissaDubbelaar reviewed Jan 8, 2026
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jonasscheid commented Jan 8, 2026

@copilot change all Channel. to channel. in all nextflow scripts in this repo

Copilot AI mentioned this pull request Jan 8, 2026
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Copilot AI commented Jan 8, 2026

@jonasscheid I've opened a new pull request, #430, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot AI and others added 2 commits January 8, 2026 15:05
@jonasscheid
Change all Channel. to channel. in Nextflow scripts
1caec35 
Co-authored-by: jonasscheid <[email protected]>
@jonasscheid
Merge pull request #430 from nf-core/copilot/sub-pr-429
b889a26 
Change Channel. to channel. in all Nextflow scripts
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jonasscheid commented Jan 8, 2026

@nf-core-bot fix linting

@jonasscheid jonasscheid mentioned this pull request Jan 8, 2026
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@jonasscheid jonasscheid changed the title Merge template 351 Merge template 3.5.1 Jan 8, 2026
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jonasscheid commented Jan 8, 2026

@copilot please update the pipeline version in all nf.test.snapshots from 3.1.0 to 3.2.0dev

   48         "Workflow": {                48         "Workflow": {            
!  49             "nf-core/mhcquant": " !  49             "nf-core/mhcquant": "
v3.1.0"                                 v3.2.0dev"                             
   50         }                            50         }                        
   51     },                               51     },                           
   52     [                                52     [

Copilot AI mentioned this pull request Jan 8, 2026
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Copilot AI commented Jan 8, 2026

@jonasscheid I've opened a new pull request, #432, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot AI and others added 2 commits January 8, 2026 17:23
@jonasscheid
Update pipeline version from v3.1.0 to v3.2.0dev in all snapshot files
e991182 
Co-authored-by: jonasscheid <[email protected]>
@jonasscheid
Merge pull request #432 from nf-core/copilot/sub-pr-429
3ff11ef 
Update pipeline version in test snapshots from v3.1.0 to v3.2.0dev
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jonasscheid commented Jan 8, 2026

Ready for review @marissaDubbelaar :)

marissaDubbelaar
marissaDubbelaar approved these changes Jan 9, 2026
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LGTM 🚀

@jonasscheid jonasscheid merged commit 359a447 into dev Jan 9, 2026
14 checks passed
@jonasscheid jonasscheid deleted the merge-template-351 branch January 9, 2026 10:56
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